differential_test: Differential testing of abundant/expression of a given...

In JacobAgerbo/QuickFixR: Helps scientist with data explorative tasks with user interface

Differential testing of abundant/expression of a given feature for a variable with two levels

Description

Differential testing of abundant/expression of a given feature for a variable with two levels

Usage

differential_test(
  MAE,
  tax_level,
  variable = c(),
  min_num_filter = 5,
  padj_cutoff = 0.05,
  sig_only = c("Yes", "No")
)

Arguments

MAE	A multi-assay experiment object
tax_level	The classification level used for feature
variable	Compare groups by binary variable e.g. 'Disease State'
min_num_filter	Filtering of minimal number of counts. Defaults to 5
padj_cutoff	Cutoff for p value adjustment, using BH. Defaults to 0.05
sig_only	Show only significant values in plot

Value

A plotly object, a ggplot object for pdf saving, and a table with statistics

Examples

data_dir = system.file('inst/extdata/Disease_Challenge.rds', package = 'QuickFixR')
df <- readRDS(data_dir)
p <- differential_test(df,
                    tax_level='Genus',
                    variable='Disease_State',
                    sig_only="No")
p

JacobAgerbo/QuickFixR documentation built on Sept. 20, 2023, 12:40 p.m.